كتب : Sherif Tarek
The victory gave Barca their sixth successive title under Josep Guardiola, who led the European champions to the maximum number of trophies this year.
Mauro Boselli headed Estudiantes in front on 37 minutes, but Pedro Rodriguez equalized one minute from time after heading home from close range.
In the 110th minute, Golden Ball winner Messi incredibly chested a Daniel Alves cross into the net to wrap up the victory and end the year in the best possible way for the Catalans.
Estudiantes hold tightly onto their slender lead, while the Spanish titans plied up pressure in the second half of the game.
Guardiola's men eventually translated their domination into goals when Rodriguez hit a late equalizer to send the game into extra-time, before Messi scored again.
Earlier this year, Barcelona won the UEFA Champions League, Primera Liga, Copa del Rey, Spanish Super Cup and European Super Cup.
South Korea's Pohang Steelers beat Mexican side Atlante on penalties to finish third in the Club World Cup earlier on the day.